Because scaffolding is a crucial form of support for students engaging in complex learning environments, it is important that researchers determine which of the numerous kinds of scaffolding will allow them to educate students most effectively. The existing literature tends to focus on computer-based scaffolding by itself rather than integrating it with teacher support. This study examined students' inquiry learning skills and content knowledge when they utilized a virtual learning environment called "Supervolcano: Kikai Caldera." The present study specifically explored how the timing of teacher-based metacognitive scaffolding in combination with different types of computer-based procedural scaffolding affected students' science inquiry learning. To answer this question, a 2 x 2 factorial design was conducted. One factor examined continuous and faded computer-based procedural scaffolds, and the other factor investigated early and late teacher-based metacognitive scaffolds. Students who received both continuous computer-based procedural scaffolding and early teacher-based metacognitive scaffolding performed best in acquiring scientific inquiry skills. Students using both faded computer-based procedural and early teacher-based metacognitive scaffolding had the worst performance in learning scientific inquiry skills. However, although we applied different types of scaffolding, the results showed no statistically significant difference among the groups' science learning knowledge. (Contains 2 figures and 6 tables.)